TOGA2: A faster, more versatile successor of Tool to infer Orthologs from Genome Alignments
The Hiller Lab at the Senckenberg Research Institute
docs .
install .
preprint .
us
runmode:- Paralog annotation is now possible even for transcripts with existing orthologous chains with
--annotate_paralogsflag. Paralogs annotated this way are retained only if they have loss status of at least UL, and no more than 5 paralogs with predicted orthologs per query locus are kept in the annotation.
- Paralog annotation is now possible even for transcripts with existing orthologous chains with
prepare-inputmode:- Annotation and isoform file can be now generated from a GFF3/GTF file;
- Minimal intron length and nonsense-mediated decay (NMD) filters for reference transcripts;
- Minimal CDS intron length filter;
- Minimal internal (non-terminal) CDS exon length filter;
- Reference gene coordinates in BED format (
${ref}.toga.genes.bed) now added to output;
integratemode:- Adding GTF format query annotation (
query_annotation.gtf.gz) to output; - Adding integration summary (
summary.txt) to output;
- Adding GTF format query annotation (
- NEW MODE:
orthogroupsenables orthogroup modelling and generates gene family files compatible with CAFE5 input. - NEW MODE:
toga2agoracreates ordered lists of 1:1 orthologs across multuple runs compatible with the AGORA tool for gene order and synteny analysis. - NEW COMPANION SCRIPT:
toga2statsfor assembly quality assessment based on the ancestral gene set. - Companion dataset:
- Adding input annotation for two turtle (Emydura macquarii macquarii, Emys orbicularis) and five percomoprh fishes (Gasterosteus aculeatus, Hippoglossus stenolepis, Melanotaenia boesemani, Nothobranchius furzeri, Synchiropus splendidus) reference species.
For the full list of code changes, see changelog.md .
TOGA2 Makefile provided in this repository contains directives for code compilation, third party software installation, Python package download, and model training.
git clone --recurse-submodules https://github.com/hillerlab/TOGA2
cd TOGA2
makeImportant
Executing the Makefile will not install Nextflow and Cargo on your machine.
Since the Make directive also installs Python packages globally, you might want to create a dedicated virtual environment beforehand (Python version 3.13 or higher):
git clone --recurse-submodules https://github.com/hillerlab/TOGA2
cd TOGA2
python3 -m venv toga2
source toga2/bin/activate
makeAs an alternative to Python virtual environment, you can also use Conda for environment creation. TOGA2 comes with a Conda configuration file which creates an environment with Python, Cargo, and Nextflow:
git clone --recurse-submodules https://github.com/hillerlab/TOGA2
cd TOGA2
conda env create -f assets/venv/conda.yaml
conda activate toga2
makeContainer image definition file for Apptainer is provided with TOGA2 under supply/containers/apptainer.def. To build the container, make sure you have Apptainer installed, then run the following commands:
git clone --recurse-submodules https://github.com/hillerlab/TOGA2
TMPDIR=${tmp_dir} apptainer build ${container.sif} supply/apptainer.defwhere:
${tmp_dir}is the path to the directory to store Nextflow temporary files in;${container.sif}is the path to save the resulting image to.
The resulting container has toga2.py as an entry point. If you run the following or similar command:
TMPDIR=${tmp_dir} apptainer run --bind ${bound_dir1},${bound_dir2} ${container.sif} toga2.pyyou should see the TOGA2 start menu.
Note
The image provided in supply/ directory contains the latest TOGA2 release, third-party software used for input preparation and TOGA2 annotation, and Nextflow for parallel process management. The container, however, does not contain any Nextflow-compatible parallel job executor. To set up your container for batch manager compatibility, see README at supply/containers and example recipe at supply/containters/apptainer_slurm.def
If activated without additional arguments (toga2.py), the following start screen is displayed in the user's terminal:
Usage: toga2.py [OPTIONS] COMMAND [ARGS]...
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TOGA2 - Tool for Ortholog Inference from Genome Alignment
Options:
-V, --version Show the version and exit.
-help, -h, --help Show this message and exit.
Commands:
cookbook List example commands for 'run' mode
from-config Run TOGA2 pipeline with a configuration file
integrate Prepare an integrated TOGA2 annotation by combining annotation with different references
merge Merge complementing TOGA2 results for the same reference and query
postoga Run postprocessing analysis with Postoga
prepare-input Prepare reference annotation files for TOGA2 input
run Run TOGA2 pipeline with command line arguments
sequence-alignment Align orthologous sequences from multiple TOGA2 results
spliceai Generate SpliceAI predictions for query assembly
test Test TOGA2 with companion dataset
Except for toga2.py test, invoking any of the listed commands without arguments also displays the help message. You can also invoke help message for TOGA2 or any of its commands with --help/-h option.
To ensure that TOGA2 was installed properly, run the following command:
toga2.py testProvided the successful installation, you will see the TOGA2 execution log printed to stdout, with the results stored at TOGA2/sample_output.
Note
If you are running TOGA2 from Apptainer, you might have to provide a custom output directory with --output/-o option to bypass the read-only container configuration:
TMPDIR=${tmp_dir} apptainer run --bind ${bound_dir1},${bound_dir2} ${container.sif} toga2.py test -o ${output_dir}